Search the KnowledgeBase

You are not logged in. We are redirecting you to our log-in page.

SYBYL-X 

SYBYL®-X 2.0 will be available for download by all currently supported SYBYL-X customers the week of March 12, 2012, and will be available by default as a software download, however, a DVD set can be provided upon request.  Click here to request a DVD set.  Molecular Data Explorer in SYBYL-X

With SYBYL-X 2.0, we introduce the Molecular Data Explorer (MDE) to make your use of SYBYL-X even more intuitive and efficient.

Early testers tell us that with the MDE, they obtained insights into their dataset in minutes that previously would have taken days.

The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization. It includes:

  • A newly re-vamped molecular spreadsheet, a molecular grid viewer, graphing and charts.
  • Structure similarity maps that provide a visual structural clustering to show activity/selectivity islands and cliffs at a glance.
  • "One click" browsing of both data and 3D structures.
  • Tight coupling of all components, allowing you to gain insights from data in minutes and to view both 2D and 3D structures with their associated data.
    • Because selection in the various components is coupled, selecting a bar in a histogram of cLogP selects and highlights the relevant structures in the spreadsheet and the molecular grid.
    • Selecting a set of highly active compounds in the spreadsheet highlights these same structures in the structure similarity map and allows you to determine whether your highly active compounds reside in one or more chemotypes.
  • The MDE remembers the state and formatting of all components so that you can quickly resume your work if you exit and return.

In the process of creating the Molecular Data Explorer, we have developed a new molecular spreadsheet to make simple tasks easier. For example:

  • A single menu allows you to Compute Multiple Properties in just a few mouse clicks.
  • 2D structures displayed directly in the molecular spreadsheet allow you to quickly visualize the chemical structure with associated data.
  • You can now easily import data and merge data from files in a wide variety of formats. For example, merge chemical structure information in SMILES format with biological data in csv or tsv format
    .
  • New capabilities to Print and Export the spreadsheet and graphs have been added.

In addition, with SYBYL-X 2.0 we have enhanced the QSAR project manager to allow you to build CoMSIA and EVA QSAR models.

Supported Platforms for this release include:

  • Mac OS-X 10.6.x (Snow Leopard)
  • 32-bit and 64-bit Windows 7, 32-bit Windows XP SP3
  • 32-bit and 64-bit Red Hat Enterprise Linux versions 5 and 6

Learn more about system requirements for SYBYL-X for Mac, Windows, or Linux.

Not using SYBYL-X today?  Read on for more information about recent releases:

SYBYL®-X 1.3 was released on May 5, 2011.

Highlights of new features made available in SYBYL-X 1.3 include:

screen shotSupport for Mac OS X
SYBYL-X is now available on the popular Mac platform, with support for the Mac OS X 10.6.x. Going forward, SYBYL-X releases will stay in sync across Windows, Linux and Mac to support your computational efforts when and where ever you need to work. Purchase a new or additional license to expand your access to modeling and simulation with SYBYL-X, or, if you have a network license, just let your Mac systems compete for your available licenses.

Support for Windows 7
SYBYL-X 1.3 also provides support for Windows 7, in addition to the traditional Windows XP.

Enhancements to the QSAR project manager include:

  • The use of SAR maps to analyze data.
  • The ability to create structure sets based on a variety of criteria.
  • The interactive display of 3D structures and graphs within the project manager.

Additional Quick Access improvement:

  • A STOP icon to interrupt interactive energy minimizations and dynamics runs.
  • Movies to provide a quick introduction to various aspects of SYBYL-X workflows.

Haven't upgraded to SYBYL-X 1.2 yet?  Read on:

SYBYL®-X 1.2 was released on October 18, 2010 for Windows and Linux, 

Highlights of new features made available in SYBYL-X 1.2 include:

  • QSAR Project Manager:  a new project-oriented interface that facilitates the creation, analysis, and application of QSAR models
    • Streamlines all phases of QSAR workflows for QSAR novices as well as experts:  Model Preparation, Descriptor Selection and Computation, Model Creation, Model Application, and Project/Model Management
    • Customers who were provided early access to the QSAR Project Manager are enthusiastic:  “For the first time, I feel confident that I am able to understand yesterday’s work the day after.  I’m able to apply CoMFA models, and the packaging and structuring of my work in the QSAR manager…. really makes me more productive.”
  • New features make the latest science in Surflex-Dock easily accessible via the SYBYL-X interface
    • Fragment Constrained Docking:  easily set up “placed fragment” constraints to guide the docking run.
    • Protein Flexibility:  Employ protein relaxation in a docking experiment to improve pose rankings
  • Better Communication to the Chemistry Desktop: SYBYL-X can now read and write structure files in Benchware 3D Explorer format to support easy transfer of information between applications

And of course, everything listed above has been built on the major redesign made available in SYBYL-X 1.1:

Enhancements in SYBYL-X 1.1 provide significant improvements in general usability, reducing by half the number of mouse clicks and by more than half the mouse travel needed for basic molecule visualization and manipulation, thereby providing a far more intuitive modeling experience.

Our overall goal while continuing development in SYBYL-X is to provide you with access to the highest quality and validated scientific techniques, so that application of CADD maximizes your productivity within an increasingly demanding working environment. We are working more closely with you to help us meet and exceed your goals for efficient accurate CADD.

The SYBYL-X strategy is three-fold:

  • Quick Access - making the basic things quick and easy
  • Workflows - simplifying and streamlining an entire workflow, from data input to presentation of results
  • Scientific Innovation - creating and delivering scientific capabilities that provide the newest and/or best of those methodologies which are most helpful in the design of bioactive molecules.

SYBYL-X 1.1 leverages the major infrastructure investments we made in the first release of
SYBYL-X in late 2009, emphasizing Quick Access to make your use of SYBYL-X more efficient and pleasurable. You will notice many improved possibilities for the basic use of SYBYL-X.  Particularly noteworthy enhancements are:

  • A new selection model that allows actions on selected entities
  • Enhanced, simplified menu systems for frequently used functions
  • Significantly updated toolbar system
  • Context sensitive (right-click) menus
  • Enhanced session saving capabilities

While the focus of this release has been Quick Access we have also made both workflow and scientific improvements:

Workflows:

  • Addition of protein preparation to the docking/virtual screening workflows
  • Addition of ligand preparation to the docking/virtual screening workflows
  • Addition of MOLCAD channel surface capabilities to active site location

Scientific improvements (in the updated Surflex-Dock version):

  • Treatment of protein flexibility in docking
  • Self-scoring term in docking scoring